Phylogenetic Analysis of DELLA Proteins

DELLA protein sequences of pumpkin (7), cucumber (4), melon (4), watermelon (4), Arabidopsis (5), soybean (7), Brassica napus (13), rice (1), tomato (2) and maize (3) were retrieved from cucurbit genomics database, TAIR and Ensembl database (http://plants.ensembl.org/index.html), respectively. Based on multiple sequence alignment, phylogenetic tree was created using the neighbor-joining (NJ) method with MEGA 7.0. The conserved domains were analyzed by the NCBI CDD, and the conserved motifs were predicted by MEME (https://meme-suite.org/meme/). Furthermore, the distribution maps of conserved domains and conserved motifs were visualized using TBtools v 1.0986961. Promoter sequences (2 kp before the start codon) of CmoDELLA genes were analyzed through online PlantCare (https://bioinformatics.psb.ugent.be/webtools/plantcare/html/) to obtain cis-regulatory elements. Interaction networks between CmoDELLA proteins and other proteins were conducted through online STRING (https://string-db.org/), using Arabidopsis as reference species.

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Luo W., Zhao Z., Chen H., Ao W., Lu L., Liu J., Li X, & Sun Y. (2023). Genome-wide characterization and expression of DELLA genes in Cucurbita moschata reveal their potential roles under development and abiotic stress. Frontiers in Plant Science, 14, 1137126.

Publication 2023

Arabidopsis Based sequence Brassica napus Cucumber Genes Maize Maps Melon Plants Protein sequences Proteins Pumpkin Regulatory elements Rice Soybean Start codon Tomato Watermelon

Corresponding Organization : Henan Institute of Science and Technology

Other organizations : Xinxiang University

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Variable analysis

independent variables

DELLA protein sequences of pumpkin (7), cucumber (4), melon (4), watermelon (4), Arabidopsis (5), soybean (7), Brassica napus (13), rice (1), tomato (2) and maize (3)

dependent variables

Phylogenetic tree created using the neighbor-joining (NJ) method
Conserved domains analyzed by the NCBI CDD
Conserved motifs predicted by MEME
Distribution maps of conserved domains and conserved motifs visualized using TBtools v 1.0986961
Cis-regulatory elements in promoter sequences (2 kp before the start codon) of CmoDELLA genes analyzed through online PlantCare
Interaction networks between CmoDELLA proteins and other proteins conducted through online STRING, using Arabidopsis as reference species

control variables

Independent variables not explicitly mentioned.
Dependent variables not explicitly mentioned.
Control variables not explicitly mentioned.

positive controls

None specified

negative controls

None specified

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